Top investigators share research findings on biological signaling mechanisms that ensure robustness and wound repair.

September 13, 2024

This summer, over 50 researchers in the NSF EMBRIO Institute convened to share their newest findings on cellular signaling and organization that drives wound repair, cellular defense, and organismal robustness.  The EMBRIO Institute stands for Emerging Mechanisms in Biology of Robustness, Integration, and Organization, is one of 15 National Science Foundation Biology Integration Institutes. Investigators in the institute use imaging, computing, and AI in several biological organisms including plant and animal systems to address core rules of life questions.   The institute includes diverse investigators studying a core biological question across several species in the plant and animal kingdoms is led by Purdue University and includes 5 additional university partners.

During the meeting, hosted at Purdue University, a new competition was held to recognize the best work around producing scientific images, live cell videos, and simulations that convey the most impact and innovation, together with the degree of explaining the biological data, mechanisms, or processes.

Ongoing research pursues questions of how living systems integrate chemical and mechanical stimuli to develop robust cells and tissues, even when those tissues are injured. Answering these challenging questions may have potentially far-reaching impacts on our understanding of organismal health across plant and animal kingdoms- the cross species sharing and integration of knowledge is an example in practice of the ONE Health initiatives at Purdue. The National Science Foundation recognized the scientific merits of this Big Idea and awarded the Institute a five-year grant in late 2021 from the Biology Integration Institutes program, launched to support unique interdisciplinary and integrative science necessary to investigate complex questions in biology.

The first-place scientific images included a submission from Bakary Samasa (University of Pennsylvania) in the Graduate Division, and in the Postdoctoral and Research Scientist Division member voting resulted in a tie between Sharon Minsuk (Indiana University, Bloomington), and Weiwei Zhang (Purdue University). Bakary’s winning entry follows up on his earlier imaging success, a scientific image that became a U.S. Postage stamp! A high level of knowledge, skill, and innovative research was involved in producing the top images, live cell videos, and modeling simulation. Readers can view the winning submissions with background information and context at the EMBRIO website.

Samasa, a doctoral candidate mentored by Professor Mary Mullins in the Perelman School of Medicine at UPenn, is conducting research to elucidate the mechanisms of epiboly. Epiboly is one of several types of cell movement during early development of animal embryos that drive the embryo’s transformation into a fully formed individual. The Mullins lab studies zebrafish to investigate epiboly. Samasa explained,

“My research focuses on how the cytoskeleton and calcium interplay to drive the process of epiboly. I’ve been learning and employing various imaging modalities as well as mutant zebrafish in my efforts to determine the mechanisms of the morphogenetic process.”

As part of the collaborative framework of EMBRIO, each graduate student has at least one co-mentor from another department or university. Professor and Institute Executive Director and PI David Umulis, serves on Bakary’s doctoral committee. In addition to the Umulis Quantitative and Systems Biology Lab at Purdue, Samasa and Mullins are actively collaborating with Sharon Minsuk in the James Glazier lab at Indiana University to develop an accurate simulation of epiboly.

Minsuk, Research Fellow in the Biocomplexity Institute at Indiana University, submitted a video of Zebrafish epiboly simulation that tied for top place in the Postdoctoral and Research Scientist Division. Minsuk, along with Professor James Glazier, and former postdoc T.J. Sego (now at University of Florida), have been incorporating the knowledge gained from experimental biology performed by Samasa and Mullins at UPenn, and Linlin Li and David Umulis in Biomedical Engineering at Purdue. The recent iteration of the simulation has been able to more closely mirror the kinds of mechanical forces occurring in live embryos. Minsuk explains,

“Embryos of all multicellular species go through a spectacular transformation from that first cell to the complex organisms they become. I’m especially interested in morphogenesis — the dramatic changes in shape of embryonic tissues that give rise to all these forms. My work is to simulate these processes in a computer, which not only tests our current understanding, but can stretch our ability to make predictions and can suggest new experiments.”

Moving from the Animal Kingdom with Zebrafish (Danio rerio) into the Plant Kingdom with Rockcress (Arabidopsis thaliana), Weiwei Zhang, Senior Plant Cell Biologist working in Chris Staiger’s  lab in Botany and Plant Pathology at Purdue, tied for first place with Minsuk in the Postdoc and Research Scientist Division.

“I study how immunity works in plants so that they are resistant to various fungal and bacterial pathogens. I am investigating how plants detect the presence of potential pathogens, and how this recognition triggers a complex network of signaling pathways inside the plant cell.”, said Zhang. “I’ve been using state-of-the-art live-cell imaging tools combined with genetic and pharmacological perturbations to better understand plant tissue defense.”

Zhang’s and Staiger’s research have led to active collaborations across the Institute, including with labs at Purdue (Anjali Iyer-Pascuzzi's  lab, Elsje Pienaar's  lab, and Taeyoon Kim's  lab), Jeremiah Zartman’s Multicellular Systems Engineering lab  at University of Notre Dame, and Mauricio Cabrera-Rios and Clara Isaza with The Applied Optimization Group at University of Puerto Rico at Mayagüez.

Interdisciplinary collaborations and team science, coupled with advances in both cell imaging technology and computational modeling of biological systems, are moving EMBRIO Institute scientists closer to a big picture understanding of how cells integrate and organize information to support robust development of tissues in the face of environmental and pathological challenges.

When asked about how collaborations in EMBRIO have benefited their own research goals, Minsuk had this to say,

"I believe a combined modeling and experimental approach can bring synergy and a deeper understanding than either approach can achieve on its own. As a former experimental embryologist and software developer moving into biophysical modeling, I couldn’t do what I’m doing without on the one hand, my experimentalist colleagues with their deep familiarity with the zebrafish embryo, and on the other hand my physicist colleagues with their theoretical insights about how to model and understand the deep underlying physical and mathematical structure of living tissue."

Asked the same question, Zhang responded,

“As an experimental biologist with little prior experience in computational modeling, the EMBRIO projects have been a transformative opportunity. Collaborating closely with computational biologists to develop models and simulations of signaling processes in plant immunity has completely changed how I view biological processes—now through a mathematical lens. This collaboration has not only deepened our understanding of the intricate dynamics of cellular signaling but also inspired new hypotheses and experiments to push our research forward.”

David Umulis, Executive Director of EMBRIO Institute, professor and researcher at Purdue, and Sr. Vice Provost of the Purdue in Indianapolis campus, has focused much of his research career on quantitative methods to understanding biological processes. Reflecting on the level of integrated interdisciplinary science necessary to make progress on Rules of Life questions, Umulis underscores the significant value that the Institute is adding to scientists’ experience,

“We’ve been able to achieve progress on the scientific questions in such a short time frame through the utilization of integrative tools such as computer simulation, AI, and shared reagents.  We also benefit from the foundation of the institute that established an inclusive, open, and collaborative framework focused on shared goals, an ambitious research target, and a new way of thinking to pursue research and academic excellence.  Our faculty and trainees are engaged in co-mentoring and learning through team science across disciplines to the benefit of our early career scientists like Mr. Samasa, Dr. Minsuk, and Dr. Zhang.”

To learn more about EMBRIO’s research and education efforts, visit the Institute’s website or Google Scholar page.

News Media Contact: email to laddb [at] purdue.edu

Writers: Brent T. Ladd, David M. Umulis